avg_probe_exp {multiClust} | R Documentation

## Function to produce a matrix containing the average expression of each gene probe within each sample cluster.

### Description

Function to produce a matrix containing the average expression of each gene probe within each sample cluster.

### Usage

    avg_probe_exp(sel.exp, samp_cluster, data_name, cluster_type = "HClust",
      distance = "euclidean", linkage_type = "ward.D2",
      probe_rank = "SD_Rank", probe_num_selection = "Fixed_Probe_Num",
      cluster_num_selection = "Fixed_Clust_Num")

### Arguments

`sel.exp` | Object containing the numeric selected gene expression matrix. This object is an output of the probe_ranking function.
`samp_cluster` | Object vector containing the samples and the cluster number they belong to. This is an output of the cluster_analysis function.
`data_name` | String indicating the cancer type and name of the dataset being analyzed. This name will be used to label the sample dendrograms and heatmap files.
`cluster_type` | String indicating the type of clustering method used in the cluster_analysis function. "Kmeans" or "HClust" are the two options.
`distance` | String describing the distance metric uses for HClust in the cluster_analysis function. Options include one of "euclidean", "maximum", manhattan", "canberra", "binary", or "minkowski".
`linkage_type` | String describing the linkage metric used in the cluster_analysis function. Options include "ward.D2", "average", "complete", "median", "centroid", "single", and "mcquitty".
`probe_rank` | String indicating the feature selection method used in the probe_ranking function. Options include "CV_Rank", "CV_Guided", "SD_Rank", and "Poly".
`probe_num_selection` | String indicating the way in which probes were selected in the number_probes function. Options include "Fixed_Probe_Num", "Percent_Probe_Num", and "Adaptive_Probe_Num".
`cluster_num_selection` | String indicating how the number of clusters were determined in the number_clusters function. Options include "Fixed_Clust_Num" and "Gap_Statistic".

### Value

Returns an object matrix with the average mean expression for each probe in each sample cluster. Also outputs the object to a text file.

### Author(s)

Nathan Lawlor, Alec Fabbri

### See Also

`number_clusters`, `number_probes`, `probe_ranking`, `cluster_analysis`

### Examples

    # Produce matrix of average expression of each probe in each cluster
    # Load in a data file
    data_file <- system.file("extdata", "GSE2034.normalized.expression.txt",
        package="multiClust")
    data <- input_file(input=data_file)
    # Choose 300 genes to select for
    gene_num <- number_probes(input=data_file, data.exp=data, Fixed=300,
       Percent=NULL, Adaptive=NULL)
    # Choose the "CV_Rank" Method for gene ranking
    sel.data <- probe_ranking(input=data_file, probe_number=300,
        probe_num_selection="Fixed_Probe_Num", data.exp=data, method="CV_Rank")
    # Choose a fixed cluster number of 3
    clust_num <- number_clusters(data.exp=data, Fixed=3, gap_statistic=NULL)
    # Call function for Kmeans parameters
    kmeans_analysis <- cluster_analysis(sel.exp=sel.data, cluster_type="Kmeans",
        distance=NULL, linkage_type=NULL, gene_distance=NULL,
        num_clusters=3, data_name="GSE2034 Breast",
        probe_rank="CV_Rank", probe_num_selection="Fixed_Probe_Num",
        cluster_num_selection="Fixed_Clust_Num")
    # Call function for average matrix expression calculation
    avg_matrix <- avg_probe_exp(sel.exp=sel.data, samp_cluster=kmeans_analysis,
        data_name="GSE2034 Breast", cluster_type="Kmeans", distance=NULL,
        linkage_type=NULL, probe_rank="CV_Rank",
        probe_num_selection="Fixed", cluster_num_selection="Fixed_Clust_Num")

[Package multiClust version 1.12.0 Index]